Nextflow Registry | nf-core/modkit/repair@0.0.0-0c7146d

nf-core/modkit/repair @ 0.0.0-0c7146d

Repair the MM/ML tags on trimmed or hard-clipped ONT reads using untrimmed ONT reads.

methylation ont long-read

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @jkh00

Maintainers: @jkh00

Repair the MM/ML tags on trimmed or hard-clipped ONT reads using untrimmed ONT reads.

Add the following snippet to your workflow script to include this module.

include { MODKIT_REPAIR } from 'nf-core/modkit/repair'

MIT License

Process

`Name`	`MODKIT_REPAIR`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`before_trim` file	Sorted BAM file `*.{bam}`
`after_trim` file	Sorted BAM file `*.{bam}`

Output 3 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.bam` file	Sorted BAM file `*.{bam}`

#2 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.log` file	File for debug logs to be written to `*.log`

#3 versions_modkit tuple

`${task.process}` string	The name of the process
`modkit` string	The name of the tool
`modkit --version \| sed 's/modkit //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
modkit	A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data.	https://nanoporetech.github.io/modkit/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:57:25 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmodkit%2Frepair/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/modkit/repair/blobs/sha256:d3fd0987cf9669e390417cff50d9d92c7f72b1d4a5c860986780d6463daa4acc
Size	2.5 KB
Checksum	sha256:d3fd0987cf9669e390417cff50d9d92c7f72b1d4a5c860986780d6463daa4acc
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:57:25 (UTC)		1	2.5 KB	-